There are so many variables in fare pricings heaven only knows what's happening here. It may be the AA system was still showing a discounted fare in it's inventory that US no longer had available. There is not one system out there feeding all the sites real-time. AA may have been told there are x economy fares available and will sell them until depleted or US sends an update to AA.

Having more details would help someone track it down a bit more. Flight numbers, dates, fare codes, systems used, etc. This is one of those corner cases that should be resolved once the reservation systems are merged. Until then you will find hiccups like this.

Good luck getting this resolved.